Tags:
Owner:
ariane.badoual@inria.fr
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
Please log in to perform a job with this app.
You must provide four SBML Files to upload and assign their roles in the Parameters:
--seeds file1.sbml--targets file2.sbml--repairnet file3.sbml--draftnet file4.sbmlFor have the list of all targets you can add in the Parameters:
--enumerateIn input :
In output :
--seeds seeds.sbml --draftnet draft.sbml --repairnet repair.sbml --targets targets.sbml --enumerate Reading draft network from draft.sbml Reading seeds from seeds.sbml Reading targets from targets.sbml Checking draftnet for unproducible targets 31 unproducible targets: M_cl_c M_pe161_p M_10fthf_c M_mobd_c M_2ohph_c M_pydx5p_c M_cys_DASH_L_c M_pe160_c M_udcpdp_c M_dctp_c M_coa_c M_pe160_p M_fad_c M_sheme_c M_met_DASH_L_c M_utp_c M_so4_c M_fe3_c M_pe161_c M_pheme_c M_datp_c M_cu2_c M_mlthf_c M_adp_c M_nad_c M_gtp_c M_nadp_c M_thf_c M_amet_c M_dgtp_c M_ribflv_c Reading repair network from repair.sbml done Checking draftnet + repairnet for unproducible targets still 29 unproducible targets: M_10fthf_c M_mobd_c M_2ohph_c M_pydx5p_c M_cys_DASH_L_c M_pe160_c M_udcpdp_c M_dctp_c M_coa_c M_pe160_p M_fad_c M_sheme_c M_met_DASH_L_c M_utp_c M_thf_c M_so4_c M_fe3_c M_pe161_c M_pheme_c M_datp_c M_mlthf_c M_adp_c M_nad_c M_gtp_c M_nadp_c M_pe161_p M_amet_c M_dgtp_c M_ribflv_c 2 targets to reconstruct: M_cu2_c M_cl_c Computing essential reactions for M_cu2_c 1 essential reactions found: R_CU2tpp Computing essential reactions for M_cl_c 1 essential reactions found: R_CLt3_2pp Overall 2 essential reactions found. R_CLt3_2pp R_CU2tpp Adding essential reactions to network. Computing one minimal completion to produce all targets R_CLt3_2pp R_CU2tpp Computing common reactions in all completion with size 2 R_CLt3_2pp R_CU2tpp Computing union of reactions from all completion with size 2 R_CLt3_2pp R_CU2tpp Computing all completions with size 2 Completion 1: R_CLt3_2pp R_CU2tpp The workdir contains: total 5336 -rw-r--r-- 1 500 500 1621 Mar 10 10:31 allgo.log -rw-r--r-- 1 500 500 1099262 Mar 10 10:30 draft.sbml -rw------- 1 500 500 1022934 Mar 10 10:31 meneco_0eptfrul.lp -rw-r--r-- 1 500 500 3280456 Mar 10 10:30 repair.sbml -rw-r--r-- 1 500 500 45485 Mar 10 10:30 seeds.sbml -rw-r--r-- 1 500 500 4256 Mar 10 10:30 targets.sbml ==== ALLGO JOB SUCCESS ====
10/03/2020 : Version 1.0, initial version
This app id is : 209
This curl command will create a job, and return your job url, and also the average execution time
files and/or dataset are optionnal, think to remove them if not wantedcurl -H 'Authorization: Token token=<your_private_token>' -X POST -F job[webapp_id]=209 -F job[param]="" -F job[queue]=standard -F files[0]=@test.txt -F files[1]=@test2.csv -F job[file_url]=<my_file_url> -F job[dataset]=<my_dataset_name> https://allgo.inria.fr/api/v1/jobs
Then, check your job to get the url files with :
curl -H 'Authorization: Token token=<your_private_token>' -X GET https://allgo.inria.fr/api/v1/jobs/<job_id>